Figure 6.

Using gene regions in a whole genome alignment to the chicken reference genome (galGal3),
we compared the number of scaffolds of each assembly that the alignment of each gene
is split between. Although many genomic rearrangements may exist between chicken and crocodile, assuming
that breakpoints tend to happen between genes rather than within genes, this method
allows us to assess the relative quality of assemblies in the same manner as Figure
5 when assembled and verified transcripts are not yet available.